I'd be inclined to try them one at a time.
Backup the registry key in question, and then delete it.
Restart your computer then check to see how many download folders you've got.
If everything is OK you're good to go. If not, restore the deleted registry key then backup and delete the other one.
I can only imagine it has occurred because you may have saved a previous download to a location other than the default downloads folder and I imagine what you're seeing is a junction point in action. The key wording is yours: "They appear double though and lead to the same location".
The other option would be a sytem restore to a point before the problem occurred.
You might find this software of use: http://www.getfoldersize.com/en_getfoldersize.htm